RetrogeneDB ID: retro_chof_15

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_255918:127..1267(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000012286
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000003460
• Aliases: None
• Description: None

Sequence

>retro_chof_15
ACCTCAGATTTTCCTGTTCTTGATCCAAGCTGGACTGCTCAAGAAGAAATGGCCCTTTTAGAAGCTGTGATGGACTGTGG
CTTTGGAAATTGGCAGGATGTAGCCAATCAGATGTGTACCAAGACCAAGGAGGAGTGTGAGAAGCACTATATGAAACATT
TCATCAACAACCCTCTGTTTGCATCTACCTTGCTGAACCTGAAGCAAGCAGAGGAAGCAAAAACTGCTGACACAGCAATT
CCGTTTCACTCTACGGATGACCCTCCCCGGCCTAACTTTGACTCTCTGCTTTCTCGGGACATGGCAGGATACATGCCAGC
TCGAGCAGACTTCATTGAGGAGTTTGACAATTATGCAGAATGGGACTTGAGAGACATCGATTTTGTTGAAGATGACTCGG
ACATTTTACATGCTCTGAAGATGGCTGTGGTAGATATCTATCATTCCAGGTTAAAAGAGAGACAAAGGCGAAAAAAAATT
ATAAGAGACCATGGATTAATCAACCTTAGAAAGTTTCAGTTAATGGAACGGCGGTATCCCAAGGAGGTCCAAGACCTTTA
TGAAACAATGAGGCGATTTGCAAGGATTGTGGGGCCGGTGGAGCATGACAAGTTCATTGAAAGCCATGCATTGGAATTTG
AACTCCGAAGGGAAATCAAGAGGCTCCAGGAATATAGGACAGCAGGCATTACCAGTTTTTGTAGTGCCAGAACCTATGAT
CACCTCAAGAAGACAAGAGAGGAGGAACGCCTTAAACGCACCATGCTCTCCGAAGTTCTCCAGTATATCCAGGACAGTAG
TGCTTGCCAGCAGTGGCTCCGCCGACAAGCCGACATTGACTCTGGCCTCAGTCCTTCCATTCCAATGGCTTCAAATTCAG
GTAGACGGAGTGCACCACCCTTGAACCTCACTGGCCTCCCTGGCACAGAGAAGCTGAATGAAAAAGAAAAAGAGCTCTGT
CAGATGGTGAGGTTGGTCCCTGGAGCCTATTTAGAATACAAATCTGCTCTATTGAATGAATGTAACAAGCAAGGAGGCTT
GAGACTGGCACAGGCAAGAGCACTGATCAAGATAGACGTGAACAAAACCCGGAAAATCTATGATTTCCTCATCCGAGAAG
GATACATCACTAAAGCCTGA

Alignment

ORF - retro_chof_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 86.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSDFPVLDPSWTAQEEMALLEAVMDCGFGNWQDVANQMCTKTKEECEKHYMKHFINNPLFASTLLNLKQA
          TSDFPVLDPSWTAQEEMALLEAVMDCGFGNWQDVANQMCTKTKEECEKHYMKHFINNPLFASTLLNLKQA
Retrocopy TSDFPVLDPSWTAQEEMALLEAVMDCGFGNWQDVANQMCTKTKEECEKHYMKHFINNPLFASTLLNLKQA

Parental  EEAKTADTAIPFHSTDDPPRPNFDSLLSRDMAGYMPARADFIEEFDNYAEWDLRDIDFVEDDSDILHALK
          EEAKTADTAIPFHSTDDPPRPNFDSLLSRDMAGYMPARADFIEEFDNYAEWDLRDIDFVEDDSDILHALK
Retrocopy EEAKTADTAIPFHSTDDPPRPNFDSLLSRDMAGYMPARADFIEEFDNYAEWDLRDIDFVEDDSDILHALK

Parental  MAVVDIYHSRLKERQRRKKIIRDHGLINLRKFQLMERRYPKEVQDLYETMRRFARIVGPVEHDKFIESHA
          MAVVDIYHSRLKERQRRKKIIRDHGLINLRKFQLMERRYPKEVQDLYETMRRFARIVGPVEHDKFIESHA
Retrocopy MAVVDIYHSRLKERQRRKKIIRDHGLINLRKFQLMERRYPKEVQDLYETMRRFARIVGPVEHDKFIESHA

Parental  LEFELRREIKRLQEYRTAGITSFCSARTYDHLKKTREEERLKRTMLSEVLQYIQDSSACQQWLRRQADID
          LEFELRREIKRLQEYRTAGITSFCSARTYDHLKKTREEERLKRTMLSEVLQYIQDSSACQQWLRRQADID
Retrocopy LEFELRREIKRLQEYRTAGITSFCSARTYDHLKKTREEERLKRTMLSEVLQYIQDSSACQQWLRRQADID

Parental  SGLSPSIPMASNSGRRSAPPLNLTGLPGTEKLNEKEKELCQMVRLVPGAYLEYKSALLNECNKQGGLRLA
          SGLSPSIPMASNSGRRSAPPLNLTGLPGTEKLNEKEKELCQMVRLVPGAYLEYKSALLNECNKQGGLRLA
Retrocopy SGLSPSIPMASNSGRRSAPPLNLTGLPGTEKLNEKEKELCQMVRLVPGAYLEYKSALLNECNKQGGLRLA

Parental  QARALIKIDVNKTRKIYDFLIREGYITKA
          QARALIKIDVNKTRKIYDFLIREGYITKA
Retrocopy QARALIKIDVNKTRKIYDFLIREGYITKA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_15 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003460	2 retrocopies	retro_chof_15 , retro_chof_2113,
Nomascus leucogenys	ENSNLEG00000002646	1 retrocopy	retro_nleu_930,